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haplotype analysis

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https://www.readbyqxmd.com/read/28430897/genetic-variants-associated-with-the-root-system-architecture-of-oilseed-rape-brassica-napus-l-under-contrasting-phosphate-supply
#1
Xiaohua Wang, Yanling Chen, Catherine L Thomas, Guangda Ding, Ping Xu, Dexu Shi, Fabian Grandke, Kemo Jin, Hongmei Cai, Fangsen Xu, Bin Yi, Martin R Broadley, Lei Shi
Breeding crops with ideal root system architecture for efficient absorption of phosphorus is an important strategy to reduce the use of phosphate fertilizers. To investigate genetic variants leading to changes in root system architecture, 405 oilseed rape cultivars were genotyped with a 60K Brassica Infinium SNP array in low and high P environments. A total of 285 single-nucleotide polymorphisms were associated with root system architecture traits at varying phosphorus levels. Nine single-nucleotide polymorphisms corroborate a previous linkage analysis of root system architecture quantitative trait loci in the BnaTNDH population...
April 19, 2017: DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes
https://www.readbyqxmd.com/read/28430826/geographic-origin-and-individual-assignment-of-shorea-platyclados-dipterocarpaceae-for-forensic-identification
#2
Chin Hong Ng, Soon Leong Lee, Lee Hong Tnah, Kevin Kit Siong Ng, Chai Ting Lee, Bibian Diway, Eyen Khoo
The development of timber tracking methods based on genetic markers can provide scientific evidence to verify the origin of timber products and fulfill the growing requirement for sustainable forestry practices. In this study, the origin of an important Dark Red Meranti wood, Shorea platyclados, was studied by using the combination of seven chloroplast DNA and 15 short tandem repeats (STRs) markers. A total of 27 natural populations of S. platyclados were sampled throughout Malaysia to establish population level and individual level identification databases...
2017: PloS One
https://www.readbyqxmd.com/read/28430103/genomic-characterization-of-recrudescent-plasmodium-malariae-after-treatment-with-artemether-lumefantrine
#3
Gavin G Rutledge, Ian Marr, G Khai Lin Huang, Sarah Auburn, Jutta Marfurt, Mandy Sanders, Nicholas J White, Matthew Berriman, Chris I Newbold, Nicholas M Anstey, Thomas D Otto, Ric N Price
Plasmodium malariae is the only human malaria parasite species with a 72-hour intraerythrocytic cycle and the ability to persist in the host for life. We present a case of a P. malariae infection with clinical recrudescence after directly observed administration of artemether/lumefantrine. By using whole-genome sequencing, we show that the initial infection was polyclonal and the recrudescent isolate was a single clone present at low density in the initial infection. Haplotypic analysis of the clones in the initial infection revealed that they were all closely related and were presumably recombinant progeny originating from the same infective mosquito bite...
August 15, 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/28429750/correlations-of-tnf-%C3%AE-gene-promoter-polymorphisms-with-the-risk-of-thymoma-associated-myasthenia-gravis-in-a-northern-chinese-han-population
#4
H-W Yang, P Lei, Y-C Xie, Z-L Han, D Li, S-H Wang, Z-L Sun
This study was performed with the aim to investigate the correlations of tumor necrosis factor-alpha (TNF-α) gene promoter polymorphisms with the risk of thymoma-associated myasthenia gravis (T-MG) in a northern Chinese Han population. Between June 2005 and June 2015, 305 MG patients (150 males and 155 females, MG group) and 293 healthy volunteers (negative control (NC) group) were enrolled in this study. Among the MG patients, there were 121 patients with thymoma-associated MG (T-MG group) and 184 without T-MG (NT-MG group)...
April 21, 2017: Cancer Gene Therapy
https://www.readbyqxmd.com/read/28427360/association-of-novel-polymorphisms-in-tmem39a-gene-with-systemic-lupus-erythematosus-in-a-chinese-han-population
#5
Xinze Cai, Wenyue Huang, Xudong Liu, Lining Wang, Yi Jiang
BACKGROUND: This study aimed to assess the association between 14 single nucleotide polymorphisms (SNPs) in six genes (IRF8, TMEM39A, IKZF3, ORMDL3, GSDMB, and ZPBP2) and systemic lupus erythematosus (SLE) in a Chinese Han population sample. METHODS: We carried out a case-control study of 415 patients with SLE and 470 healthy controls without autoimmune disease or cancer. DNA for genetic analysis was isolated from the blood of all subjects using standard phenol-chloroform method...
April 20, 2017: BMC Medical Genetics
https://www.readbyqxmd.com/read/28427357/haplotype-of-non-synonymous-mutations-within-il-23r-is-associated-with-susceptibility-to-severe-malaria-anemia-in-a-p-falciparum-holoendemic-transmission-area-of-kenya
#6
Elly O Munde, Evans Raballah, Winnie A Okeyo, John M Ong'echa, Douglas J Perkins, Collins Ouma
BACKGROUND: Improved understanding of the molecular mechanisms involved in pediatric severe malarial anemia (SMA) pathogenesis is a crucial step in the design of novel therapeutics. Identification of host genetic susceptibility factors in immune regulatory genes offers an important tool for deciphering malaria pathogenesis. The IL-23/IL-17 immune pathway is important for both immunity and erythropoiesis via its effects through IL-23 receptors (IL-23R). However, the impact of IL-23R variants on SMA has not been fully elucidated...
April 20, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28427149/interaction-between-ppar-%C3%AE-and-sorl1-gene-with-late-onset-alzheimer-s-disease-in-chinese-han-population
#7
Hui Zhang, Wei Zheng, Linlin Hua, Yutong Wang, Jinfeng Li, Hongying Bai, Shanshan Wang, Mingyao Du, Xuelian Ma, Chunyang Xu, Xiaodong Li, Bin Gong, Yunliang Wang
AIMS: To investigate the impact of sortilin-related receptor 1 gene 1 (SORL1) and peroxisome proliferator activated receptor gamma (PPAR G) gene single nucleotide polymorphisms (SNPs), gene- gene and gene- environment interactions and haplotype on late-onset Alzheimer's disease (LOAD) risk. METHODS: Hardy-Weinberg equilibrium (HWE), haplotype analysis and pairwise linkage disequilibrium (LD) analysis were investigated by using SNPStats (available online at http://bioinfo...
February 25, 2017: Oncotarget
https://www.readbyqxmd.com/read/28425253/association-of-the-cetp-gene-taqib-and-d442g-polymorphisms-with-essential-hypertension-in-the-chinese-mongolian-population
#8
Shudong Niu, Xiaoming Tao, Jingping Li, Yongyue Liu, Jian Wang, Mingyu Cong, Keyong Zhang, Wenyu Zhou, Changchun Qiu
BACKGROUND/AIM: This study aimed to explore the associations of the cholesteryl ester transfer protein (CETP) gene TaqIB and D442G polymorphisms with essential hypertension (EH). MATERIALS AND METHODS: In this case-control study, 883 hypertensive patients and 1044 normal controls were randomly selected from the Mongolian population of China. Polymerase chain reaction (PCR) and direct sequencing of PCR products were used to identify the genotypes. Haplotype analysis was performed by estimating the haplotype frequencies using the online SHEsis package...
April 18, 2017: Turkish Journal of Medical Sciences
https://www.readbyqxmd.com/read/28425126/novel-sequence-variants-in-the-liph-and-lpar6-genes-underlies-autosomal-recessive-woolly-hair-hypotrichosis-in-consanguineous-families
#9
Farooq Ahmad, Salma Sharif, Muhammad Furqan Ubaid, Khadim Shah, Muhammad Nasim Khan, Muhammad Umair, Zahid Azeem, Wasim Ahmad
Autosomal-recessive woolly hair/hypotrichosis (ARWH/H) is a rare genetic disorder of hair caused by variants in the LIPH and LPAR6 genes. The disease is characterized by congenital tightly curled hair leading to sparse hair later in life. In the present report genetic characterization of three consanguineous families of Pakistani origin, displaying clinical features of ARWH/H, was performed. Haplotype and DNA sequence analysis of the LIPH gene revealed a novel homozygous nonsense variant (c.688C > T; p...
April 19, 2017: Congenital Anomalies
https://www.readbyqxmd.com/read/28424495/significance-of-genetic-polymorphisms-in-long-non-coding-rna-ac079767-4-in-tuberculosis-susceptibility-and-clinical-phenotype-in-western-chinese-han-population
#10
Zhenzhen Zhao, Mei Zhang, Jun Ying, Xuejiao Hu, Jingya Zhang, Yanhong Zhou, Yi Zhou, Xingbo Song, Binwu Ying
Recent studies have implicated long non-coding RNA, AC079767.4, as a highly susceptible gene in tuberculosis. The aim of the study was to preliminarily explore the possible association of single nucleotide polymorphisms (SNPs) in AC079767.4 gene with clinical phenotypes and TB susceptibility in Western Chinese Han population. The improved multiplex ligation detection reaction (iMLDR) method was employed to genotype 4 SNPs in AC079767.4 in 554 tuberculosis patients and 561 healthy individuals. In subgroup analysis, only the C allele for rs12477677 was associated with the decreased susceptibility to pulmonary TB with a p-value of 0...
April 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28424482/logistic-bayesian-lasso-for-genetic-association-analysis-of-data-from-complex-sampling-designs
#11
Yuan Zhang, Jonathan N Hofmann, Mark P Purdue, Shili Lin, Swati Biswas
Detecting gene-environment interactions with rare variants is critical in dissecting the etiology of common diseases. Interactions with rare haplotype variants (rHTVs) are of particular interest. At the same time, complex sampling designs, such as stratified random sampling, are becoming increasingly popular for designing case-control studies, especially for recruiting controls. The US Kidney Cancer Study (KCS) is an example, wherein all available cases were included while the controls at each site were randomly selected from the population by frequency matching with cases based on age, sex and race...
April 20, 2017: Journal of Human Genetics
https://www.readbyqxmd.com/read/28424424/leukocyte-telomere-length-related-genetic-variants-in-acyp2-contribute-to-the-risk-of-esophageal-carcinoma-in-chinese-han-population
#12
Quan Fang, Lihong Hui, Zhaorui Min, Lifeng Liu, Yuan Shao
BACKGROUND: Short leukocyte telomere length has been associated with significantly increased risk of esophageal carcinoma. A previous genome-wide association study demonstrated that ACYP2 was associated with leukocyte telomere length. However, the role of ACYP2 genetic variants on esophageal carcinoma susceptibility is still unknown. Therefore, we investigated whether ACYP2 polymorphisms have impact on the risk of esophageal carcinoma in Chinese. MATERIALS AND METHODS: We conducted a case-control study among 386 cases and 495 healthy controls from northwest China...
March 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28424214/functional-conservation-and-divergence-among-homoeologs-of-taspl20-and-taspl21-two-sbp-box-genes-governing-yield-related-traits-in-hexaploid-wheat
#13
Bin Zhang, Weina Xu, Xia Liu, Xinguo Mao, Ang Li, Jingyi Wang, Xiaoping Chang, Xueyong Zhang, Ruilian Jing
Maintaining high and stable yields has become an increasing challenge in wheat breeding due to climate change. Although Squamosa-promoter binding protein (SBP)-box genes have important roles in plant development, very little is known about the actual biological functions of wheat SBP-box family members. Here, we dissect the functional conservation, divergence and exploitation of homoeologs of two paralogous TaSPL wheat loci during domestication and breeding. TaSPL20 and TaSPL21 were highly expressed in the lemma and palea...
April 19, 2017: Plant Physiology
https://www.readbyqxmd.com/read/28423715/a-functional-variant-at-the-mirna-binding-site-in-hmgb1-gene-is-associated-with-risk-of-oral-squamous-cell-carcinoma
#14
Chiao-Wen Lin, Ying-Erh Chou, Chia-Ming Yeh, Shun-Fa Yang, Chun-Yi Chuang, Yu-Fan Liu
Oral squamous cell carcinoma (OSCC) is a common malignancy that has been causally associated with both hereditary and acquired factors. The high mobility group box 1 (HMGB1) gene plays an important role as a DNA chaperone to help maintain nuclear homeostasis. Altered expression of HMGB1 has been implicated in a wide range of pathological processes, including inflammation and cancer. The present study explores the impact of HMGB1 gene polymorphisms, combined with environmental risks regarding susceptibility to oral tumorigenesis...
March 11, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423629/polymorphisms-in-human-telomerase-reverse-transcriptase-htert-gene-gene-gene-and-gene-smoking-interaction-with-susceptibility-to-gastric-cancer-in-chinese-han-population
#15
Jian Zhang, Hui Ju, Jun-Ru Gao, Xue-Long Jiao, Yun Lu
AIMS: To investigate the association of telomerase reverse transcriptase (TERT) gene polymorphisms and additional gene-gene and gene- environment interaction with gastric cancer (GC) risk. RESULTS: GC risk was significantly higher in carriers of G allele of rs2736100 than those with TT genotype (TG+ GG versus TT), adjusted OR (95%CI) =1.68 (1.26-2.17), and higher in carriers of G allele of rs2853669 than those with AA genotype (AG+ GG versus AA), adjusted OR (95%CI) = 1...
March 21, 2017: Oncotarget
https://www.readbyqxmd.com/read/28423003/hacdivsel-two-new-methods-haplotype-based-and-outlier-based-for-the-detection-of-divergent-selection-in-pairs-of-populations
#16
Antonio Carvajal-Rodríguez
The detection of genomic regions involved in local adaptation is an important topic in current population genetics. There are several detection strategies available depending on the kind of genetic and demographic information at hand. A common drawback is the high risk of false positives. In this study we introduce two complementary methods for the detection of divergent selection from populations connected by migration. Both methods have been developed with the aim of being robust to false positives. The first method combines haplotype information with inter-population differentiation (FST)...
2017: PloS One
https://www.readbyqxmd.com/read/28422522/molecular-genetic-characterization-of-a-chinese-family-with-severe-split-hand-foot-malformation
#17
Lihua Cao, Wei Yang, Shusen Wang, Chen Chen, Xue Zhang, Yang Luo
AIMS: Split hand/foot malformation (SHFM) is a congenital limb malformation characterized by underdeveloped or absent central digital rays, clefts of the hands and feet, and variable syndactyly of the remaining digits. SHFM is a genetically heterogeneous disease; the aim of this study was to identify pathogenic variations in a Chinese family with SHFM. MATERIALS AND METHODS: Haplotype analyses with microsatellite markers covering the five SHFM loci were performed to localize the causative locus...
April 19, 2017: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/28422281/wnk1-hsn2-founder-mutation-in-patients-with-hereditary-sensory-and-autonomic-neuropathy-a-japanese-cohort-study
#18
Jun-Hui Yuan, Akihiro Hashiguchi, Akiko Yoshimura, Norio Sakai, Masanori P Takahashi, Takehiro Ueda, Akira Taniguchi, Sayaka Okamoto, Nobuo Kanazawa, Yuki Yamamoto, Kazumasa Saigoh, Susumu Kusunoki, Masahiro Ando, Yu Hiramatsu, Yuji Okamoto, Hiroshi Takashima
The clinical and genetic spectrum of hereditary sensory and autonomic neuropathy (HSAN) is still unknown in Japan. We collected a broad cohort of 33 unrelated patients with predominant sensory and/or autonomic dysfunctions, who were referred to our genetic laboratory. A gene panel sequencing targeting 18 HSAN-related genes was performed using a next-generation sequencing system. A recurrent frame shift mutation in the WNK1/HSN2 gene, c.3237_3238insT (p.Asp1080*), was detected in five patients. This mutation was homozygous in four cases and of a compound heterozygous genotype in one case...
April 19, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28422000/fibromyalgia-in-300-adult-index-patients-with-primary-immunodeficiency
#19
James C Barton, Luigi F Bertoli, Jackson C Barton, Ronald T Acton
OBJECTIVES: We sought to determine the prevalence and clinical and laboratory associations of fibromyalgia in adults with primary immunodeficiency (immunoglobulin (Ig) G subclass deficiency (IgGSD) and common variable immunodeficiency (CVID). METHODS: We performed a retrospective analysis of these observations in 300 non-Hispanic white adult index patients with recurrent/severe respiratory tract infections and IgGSD or CVID: age; sex; IgGSD; fibromyalgia; chronic fatigue; autoimmune conditions (ACs); interstitial cystitis (IC); diabetes; body mass index; serum Ig isotypes; blood lymphocytes and subsets; and human leukocyte antigen (HLA)-A and -B types and haplotypes...
April 19, 2017: Clinical and Experimental Rheumatology
https://www.readbyqxmd.com/read/28421086/association-analysis-of-markers-derived-from-starch-biosynthesis-related-genes-with-starch-physicochemical-properties-in-the-usda-rice-mini-core-collection
#20
Kehu Li, Jinsong Bao, Harold Corke, Mei Sun
Rice eating and cooking quality is largely determined by starch physicochemical properties. The diverse accessions in the USDA rice mini-core collection (URMC) facilitate extensive association analysis of starch physicochemical properties with molecular markers specific to starch biosynthesis related genes. To identify significant trait-marker associations that can be utilized in rice breeding programs for improved starch quality, we conducted two association analyses between 26 molecular markers derived from starch biosynthesis related genes and 18 parameters measured of starch physicochemical properties in two sets of the mini-core accessions successfully grown in two environments in China...
2017: Frontiers in Plant Science
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